diff --git a/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java b/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
new file mode 100755
index 000000000..e4d06cad5
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/tools/FastqToBam.java
@@ -0,0 +1,180 @@
+package org.broadinstitute.sting.playground.tools;
+
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.cmdline.Option;
+import net.sf.samtools.*;
+
+import java.io.*;
+import java.util.zip.GZIPInputStream;
+import java.util.Iterator;
+
+import org.broadinstitute.sting.utils.StingException;
+
+class FastqRecord {
+    private String seqHeader;
+    private String seqLine;
+    private String qualHeader;
+    private String qualLine;
+
+    private String accessionName;
+    private String readName;
+    private String runName;
+
+    public FastqRecord(BufferedReader in) {
+        try {
+            if (in.ready()) {
+                seqHeader = in.readLine();
+                seqLine = in.readLine();
+                qualHeader = in.readLine();
+                qualLine = in.readLine();
+
+                String[] seqHeaderPieces = seqHeader.split("\\s+");
+                accessionName = seqHeaderPieces[0];
+                readName = seqHeaderPieces[1];
+
+                String[] readNamePieces = readName.split(":");
+                runName = readNamePieces[0];
+            }
+        } catch (IOException e) {
+            throw new StingException("Could not read from fastq file.");
+        }
+    }
+
+    public String getReadName() { return readName; }
+    public String getRunName() { return runName; }
+    public String getReadString() { return seqLine; }
+    public String getBaseQualityString() { return qualLine; }
+
+    public String toString() {
+        return String.format("%s %s : %s : %s", accessionName, readName, seqLine, qualLine);
+    }
+}
+
+class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord> {
+    private BufferedReader in;
+    private FastqRecord nextRecord;
+    private String runName;
+
+    public FastqReader(File file) {
+        try {
+            in = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file))));
+
+            nextRecord = new FastqRecord(in);
+            runName = nextRecord.getRunName();
+        } catch (IOException e) {
+            throw new StingException("IO problem");
+        }
+    }
+
+    public String getRunName() { return runName; }
+
+    public boolean hasNext() { return nextRecord != null; }
+
+    public FastqRecord next() {
+        FastqRecord rec = nextRecord;
+
+        try {
+            if (in.ready()) {
+                nextRecord = new FastqRecord(in);
+            } else {
+                nextRecord = null;
+            }
+        } catch (IOException e) {
+            throw new StingException("IO problem");
+        }
+        
+        return rec;
+    }
+
+    public void remove() { throw new UnsupportedOperationException("Unsupported operation"); }
+
+    public Iterator<FastqRecord> iterator() { return this; }
+}
+
+public class FastqToBam extends CommandLineProgram {
+    @Usage(programVersion="1.0") public String USAGE = "Extracts read sequences and qualities from the input fastq file and writes them into the output file in unaligned BAM format.";
+
+    @Option(shortName="I1", doc="Input file (fastq.gz) to extract reads from (single-end fastq or, if paired, first end of the pair fastq).", optional=false) public File IN1 = null;
+    @Option(shortName="I2", doc="Input file (fastq.gz) to extract reads from (if paired, second end of the pair fastq).", optional=true) public File IN2 = null;
+    @Option(shortName="O", doc="Output file (bam).", optional=false) public File OUT = null;
+    @Option(shortName="RG", doc="Read group name", optional=false) public String READ_GROUP_NAME;
+    @Option(shortName="SM", doc="Sample name", optional=false) public String SAMPLE_NAME;
+    @Option(shortName="V", doc="Verbose mode", optional=true) public Boolean VERBOSE = false;
+
+    public static void main(final String[] argv) {
+        System.exit(new FastqToBam().instanceMain(argv));
+    }
+
+    protected int doWork() {
+        FastqReader end1 = new FastqReader(IN1);
+        FastqReader end2 = (IN2 == null) ? null : new FastqReader(IN2);
+
+        SAMReadGroupRecord srg = new SAMReadGroupRecord(READ_GROUP_NAME);
+        srg.setSample(SAMPLE_NAME);
+
+        SAMFileHeader sfh = new SAMFileHeader();
+        sfh.addReadGroup(srg);
+        sfh.setSortOrder(SAMFileHeader.SortOrder.queryname);
+
+        SAMFileWriter sfw = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(sfh, false, OUT);
+
+        int readsSeen = 0;
+        while (end1.hasNext() && (end2 == null || end2.hasNext())) {
+            FastqRecord fqr1 = end1.next();
+            FastqRecord fqr2 = (end2 == null) ? null : end2.next();
+
+            if (fqr2 != null && !fqr1.getReadName().equalsIgnoreCase(fqr2.getReadName())) {
+                //throw new StingException(String.format("In paired mode, but end 1 read name (%s) does not match end 2 read name (%s)", fqr1.getReadName(), fqr2.getReadName()));
+            }
+
+            SAMRecord sr1 = new SAMRecord(sfh);
+            sr1.setReadName(fqr1.getReadName());
+            sr1.setReadString(fqr1.getReadString());
+            sr1.setBaseQualityString(fqr1.getBaseQualityString());
+            sr1.setReadUmappedFlag(true);
+            sr1.setReadPairedFlag(false);
+            sr1.setAttribute("RG", READ_GROUP_NAME);
+
+            SAMRecord sr2 = null;
+
+            if (fqr2 != null) {
+                sr1.setReadPairedFlag(true);
+                sr1.setFirstOfPairFlag(true);
+                sr1.setSecondOfPairFlag(false);
+                sr1.setMateUnmappedFlag(true);
+
+                sr2 = new SAMRecord(sfh);
+
+                sr2.setReadName(fqr2.getReadName());
+                sr2.setReadString(fqr2.getReadString());
+                sr2.setBaseQualityString(fqr2.getBaseQualityString());
+                sr2.setReadUmappedFlag(true);
+                sr2.setReadPairedFlag(true);
+                sr2.setFirstOfPairFlag(false);
+                sr2.setSecondOfPairFlag(false);
+                sr2.setMateUnmappedFlag(true);
+                sr2.setAttribute("RG", READ_GROUP_NAME);
+            }
+
+            sfw.addAlignment(sr1);
+            if (fqr2 != null) {
+                sfw.addAlignment(sr2);
+            }
+            readsSeen++;
+
+            if (VERBOSE) {
+                //System.out.println(fqr1);
+                //if (fqr2 != null) { System.out.println(fqr2); }
+                System.out.println(sr1.format());
+                if (fqr2 != null) { System.out.println(sr2.format()); }
+            }
+        }
+
+        sfw.close();
+
+        System.out.println(String.format("%s %s : processed %d reads\n", READ_GROUP_NAME, SAMPLE_NAME, readsSeen));
+
+        return 0;
+    }
+}